Biodegradation of BTEX at high salinity by an enrichment culture from hypersaline sediments of Rozel Point at Great Salt Lake

Oily bilge water treatment using indigenous soil bacteria: Implications for recycling the treated sludge in vegetable farming

Hydrocarbon contamination from motorized vessels operating on seas threaten marine ecosystems and need to treated efficiently. A bilge wastewater treatment using indigenous bacteria isolated from oil contaminated soil was studied. Five bacterial isolates (Acinetobacter baumanni, Klebsiella aerogenes, Pseudomonas fluorescence, Bacillus subtilis and Brevibacterium linens) were isolated from port soil and used in the bilge water treatment. Their crude oil degradation abilities were first confirmed experimentally. The single species and the consortia of each two species were compared in an experiment where the conditions were first optimized. The optimized conditions were 40 °C, carbon source glucose, nitrogen source ammonium chloride, pH 8, and salinity 25%. Each of the species and each combination was able to degrade oil. K. aerogenes and P. fluorescence were the most efficient in reducing the crude oil concentration. The crude oil concentration was reduced from 290 mg/L to 23 mg/L and 21 mg/L, respectively. The respective values for the loss in turbidity were from 320 NTU to 29 mg/L and 27 NTU and for BOD loss from 210 mg/L to 18 mg/L and 16 mg/L. Mn was reduced from 25.4 mg/L to 1.2 mg/L and 1.0 mg/L, Cu from 26.8 mg/L to 2.9 mg/L and 2.4 mg/L, and Pb from 29.8 mg/L to 1.5 mg/L and 1.8 mg/L. The consortium of K. aerogenes and P. fluorescence in the bilge wastewater treatment reduced the crude oil concentration to 11 mg/L. After the treatment, the water was removed and the sludge was composted with palm molasses and cow dung. After 60 days of composting and inoculation with different bacterial consortia, the final product was used as a seedbed for vegetables. The compost with the consortium K. aerogenes and P. fluorescence promoted vegetable plant growth most and could be used in farming.

Biotechnological potential of microorganisms isolated from the salar del hombre muerto, Argentina

Bacterial strains were isolated from soil and aqueous solution samples from the Salar del Hombre Muerto, Argentina. A total of 141 strains were characterized and the tolerance to sodium chloride was evaluated. We performed a screening to search for molecules of biotechnological interest: carotenoids (11%), emulsifiers (95%), and exopolysaccharides (6%), and to assess the production of enzymes, including proteolytic (39%), lipolytic (26%), hemolytic (50%), and catalase activities (99%); 25 bacterial strains were selected for further studies. Some of them produced biofilms, but only Bacillus sp. HA120b showed that ability in all the conditions assayed. Although 21 strains were able to form emulsions, the emulsifying index Kocuria sp. M9 and Bacillus sp. V3a cultures were greater than 50% and, emulsions were more stable when the bacteria grew in higher salt concentrations. Only pigmented Kocuria sp. M9 showed lipolytic activity on olive oil medium and was able to produce biofilms when cultured without and with 4 M of NaCl. Yellow pigments, lipase activity, and biosurfactant production were observed for Micrococcus sp. SX120. Summarizing, we found that the selected bacteria produced highly interesting molecules with diverse industrial applications and, many of them are functional in the presence of high salt concentrations.

Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review

Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.

Enzymatic biodegradation of highly p-xylene contaminated soil using cold-active enzymes: A soil column study

Enzymatic bioremediation is a sustainable and environment-friendly method for the clean-up of contaminated soil and water. In the present study, enzymatic bioremediation was designed using cold-active enzymes (psychrozymes) which catalyze oxidation steps of p-xylene biodegradation in highly contaminated soil (initial concentration of 13,000 mg/kg). The enzymes were obtained via co-culture of two psychrophilic Pseudomonas strains and characterized by kinetic studies and tandem LC-MS/MS. To mimic in situ application of enzyme mixture, bioremediation of p-xylene contaminated soil was carried out in soil column (140 mL) tests with the injection (3 pore volume) of different concentrations of enzyme cocktails (X, X/5, and X/10). Enzyme cocktail in X concentration contained about 10 U/mL of xylene monooxygenase (XMO) and 20 U/mL of catechol 2, 3 dioxygenases (C2,3D). X/5 and X/10 correspond to 5x and 10x dilution of enzyme cocktail respectively. The results showed that around 92-94% p-xylene removal was achieved in the treated soil column with enzyme concentration X, X/5 after second enzyme injection. While the p-xylene removal rate obtained by X/10 concentration of enzyme was less than 30% and near to untreated soil column (22.2%). The analysis of microbial diversity and biotoxicity assay (root elongation and seed germination) confirmed the advantage of using enzymes as a green and environmentally friendly approach for decontamination of pollutants with minimal or even positive effects on microbial community and also enrichment of soil after treatment.

Occurrence and biodegradation of hydrocarbons at high salinities

Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.

Carbonate facies-specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT

Organic and inorganic stable isotopes of lacustrine carbonate sediments are commonly used in reconstructions of ancient terrestrial ecosystems and environments. Microbial activity and local hydrological inputs can alter porewater chemistry (e.g., pH, alkalinity) and isotopic composition (e.g., δ¹⁸ O_water , δ¹³ C_DIC ), which in turn has the potential to impact the stable isotopic compositions recorded and preserved in lithified carbonate. The fingerprint these syngenetic processes have on lacustrine carbonate facies is yet unknown, however, and thus, reconstructions based on stable isotopes may misinterpret diagenetic records as broader climate signals. Here, we characterize geochemical and stable isotopic variability of carbonate minerals, organic matter, and water within one modern lake that has known microbial influences (e.g., microbial mats and microbialite carbonate) and combine these data with the context provided by 16S rRNA amplicon sequencing community profiles. Specifically, we measure oxygen, carbon, and clumped isotopic compositions of carbonate sediments (δ¹⁸ O_carb , δ¹³ C_carb , ∆₄₇ ), as well as carbon isotopic compositions of bulk organic matter (δ¹³ C_org ) and dissolved inorganic carbon (DIC; δ¹³ C_DIC ) of lake and porewater in Great Salt Lake, Utah from five sites and three seasons. We find that facies equivalent to ooid grainstones provide time-averaged records of lake chemistry that reflect minimal alteration by microbial activity, whereas microbialite, intraclasts, and carbonate mud show greater alteration by local microbial influence and hydrology. Further, we find at least one occurrence of ∆₄₇ isotopic disequilibrium likely driven by local microbial metabolism during authigenic carbonate precipitation. The remainder of the carbonate materials (primarily ooids, grain coatings, mud, and intraclasts) yield clumped isotope temperatures (T(∆₄₇ )), δ¹⁸ O_carb , and calculated δ¹⁸ O_water in isotopic equilibrium with ambient water and temperature at the time and site of carbonate precipitation. Our findings suggest that it is possible and necessary to leverage diverse carbonate facies across one sedimentary horizon to reconstruct regional hydroclimate and evaporation-precipitation balance, as well as identify microbially mediated carbonate formation.

Influence of salinity on the degradation of xenobiotic compounds in rhizospheric mangrove soil

Mangroves are highly productive tropical ecosystems influenced by seasonal and daily salinity changes, often exposed to sewage contamination, oil spills and heavy metals, among others. There is limited knowledge of the influence of salinity on the ability of microorganisms to degrade xenobiotic compounds. The aim of this study were to determine the salinity influence on the degradation of xenobiotic compounds in a semi-arid mangrove in La Guajira-Colombia and establish the more abundant genes and degradation pathways. In this study, rhizospheric soil of Avicennia germinans was collected in three points with contrasting salinity (4H, 2 M and 3 L). Total DNA extraction was performed and shotgun sequenced using the Illumina HiSeq technology. We annotated 507,343 reads associated with 21 pathways and detected 193 genes associated with the degradation of xenobiotics using orthologous genes from the KEGG Orthology (KO) database, of which 16 pathways and 113 genes were influenced by salinity. The highest abundances were found in high salinity. The degradation of benzoate showed the highest abundance, followed by the metabolism of the drugs and the degradation of chloroalkane and chloroalkene. The majority of genes were associated with phase I degradation of xenobiotics. The most abundant genes were acetyl-CoA C-acetyltransferase (atoB), catalase-peroxidase (katG) and GMP synthase (glutamine-hydrolysing) (guaA). In conclusion, the metagenomic analysis detected all the degradation pathways of xenobiotics of KEGG and 59% of the genes associated with these pathways were influenced by salinity.

Evaluation of sediment contamination by monoaromatic hydrocarbons in the coastal lagoons of Gulf of Saros, NE Aegean Sea

The concentrations and distribution of monoaromatic hydrocarbons (benzene, toluene, ethyl benzene and the sum of m-, p- and o-, xylenes) were determined in the sediments of coastal lagoons of the Gulf of Saros, using a static headspace GC-MS. The total concentrations of BTEX compounds ranged from 368.5 to below detection limit 0.6μgkg^-1 dw, with a mean value of 61.5μgkg^-1 dw. The light aromatic fraction of m-, p-xylene was the most abundant compound (57.1% in average), and followed by toluene (38.1%)>ethylbenzene (4.1%)>o-xylene (2.5%)>benzene (1.1%). The factor analysis indicated that the levels and distribution of BTEX compounds depend on the type of contaminant source (mobile/point), absorbance of compounds in sediment, and mobility of benzene compound and degradation processes. Point sources are mainly related to agricultural facilities and port activities while the dispersion of compounds are related with their solubility, volatility and effect of sea/saline waters on lagoons.

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah

A railroad causeway across Great Salt Lake, Utah (GSL), has restricted water flow since its construction in 1959, resulting in a more saline North Arm (NA; 24%-31% salinity) and a less saline South Arm (SA; 11%-14% salinity). Here, we characterized microbial carbonates collected from the SA and the NA to evaluate the effect of increased salinity on community composition and abundance and to determine whether the communities present in the NA are still actively precipitating carbonate or if they are remnant features from prior to causeway construction. SSU rRNA gene abundances associated with the NA microbialite were three orders of magnitude lower than those associated with the SA microbialite, indicating that the latter community is more productive. SSU rRNA gene sequencing and functional gene microarray analyses indicated that SA and NA microbialite communities are distinct. In particular, abundant sequences affiliated with photoautotrophic taxa including cyanobacteria and diatoms that may drive carbonate precipitation and thus still actively form microbialites were identified in the SA microbialite; sequences affiliated with photoautotrophic taxa were in low abundance in the NA microbialite. SA and NA microbialites comprise smooth prismatic aragonite crystals. However, the SA microbialite also contained micritic aragonite, which can be formed as a result of biological activity. Collectively, these observations suggest that NA microbialites are likely to be remnant features from prior to causeway construction and indicate a strong decrease in the ability of NA microbialite communities to actively precipitate carbonate minerals. Moreover, the results suggest a role for cyanobacteria and diatoms in carbonate precipitation and microbialite formation in the SA of GSL.

Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters

Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

Microbial community structure analysis of a benzoate-degrading halophilic archaeal enrichment

A benzoate-degrading archaeal enrichment was developed using sediment samples from Rozel Point at Great Salt Lake, UT. The enrichment degraded benzoate as the sole carbon source at salinity ranging from 2.0 to 5.0 M NaCl with highest rate of degradation observed at 4.0 M. The enrichment was also tested for its ability to grow on other aromatic compounds such as 4-hydroxybenzoic acid (4-HBA), gentisic acid, protocatechuic acid (PCA), catechol, benzene and toluene as the sole sources of carbon and energy. Of these, the culture only utilized 4-HBA as the carbon source. To determine the initial steps in benzoate degradation pathway, a survey of ring-oxidizing and ring-cleaving genes was performed using degenerate PCR primers. Results showed the presence of 4-hydroxybenzoate 3-monooxygenase (4-HBMO) and protocatechuate 3, 4-dioxygenase (3,4-PCA) genes suggesting that the archaeal enrichment might degrade benzoate to 4-HBA that is further converted to PCA by 4-HBMO and, thus, formed PCA would undergo ring-cleavage by 3,4-PCA to form intermediates that enter the Krebs cycle. Small subunit rRNA gene-based diversity survey revealed that the enrichment consisted entirely of class Halobacteria members belonging to the genera Halopenitus, Halosarcina, Natronomonas, Halosimplex, Halorubrum, Salinarchaeum and Haloterrigena. Of these, Halopenitus was the dominant group accounting for almost 91 % of the total sequences suggesting their potential role in degrading oxygenated aromatic compounds at extreme salinity.

Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium

Study of enzymes in halophiles will help to understand the mechanism of aromatic hydrocarbons degradation in saline environment. In this study, two novel catechol 2,3-dioxygenases (C23O1 and C23O2) were cloned and overexpressed from a halophilic bacterial consortium enriched from an oil-contaminated saline soil. Phylogenetic analysis indicated that the novel C23Os and their relatives formed a new branch in subfamily I.2.A of extradiol dioxygenases and the sequence differences were further analyzed by amino acid sequence alignment. Two enzymes with the halotolerant feature were active over a range of 0–30% salinity and they performed more stable at high salinity than in the absence of salt. Surface electrostatic potential and amino acids composition calculation suggested high acidic residues content, accounting for their tolerance to high salinity. Moreover, two enzymes were further characterized. The enzymes activity both increased in the presence of Fe³⁺, Fe²⁺, Cu²⁺ and Al³⁺ and showed no significant inhibition by other tested metal ions. The optimal temperatures for the C23Os were 40 °C and 60 °C and their best substrates were catechol and 4-methylcatechol respectively. As the firstly isolated and characterized catechol dioxygenases from halophiles, the two halotolerant C23Os presented novel characteristics suggesting their potential application in aromatic hydrocarbons biodegradation.

Biodegradation of organic pollutants in saline wastewater by halophilic microorganisms: a review

Agro-food, petroleum, textile, and leather industries generate saline wastewater with a high content of organic pollutants such as aromatic hydrocarbons, phenols, nitroaromatics, and azo dyes. Halophilic microorganisms are of increasing interest in industrial waste treatment, due to their ability to degrade hazardous substances efficiently under high salt conditions. However, their full potential remains unexplored. The isolation and identification of halophilic and halotolerant microorganisms from geographically unrelated and geologically diverse hypersaline sites supports their application in bioremediation processes. Past investigations in this field have mainly focused on the elimination of polycyclic aromatic hydrocarbons and phenols, whereas few studies have investigated N-aromatic compounds, such as nitro-substituted compounds, amines, and azo dyes, in saline wastewater. Information regarding the growth conditions and degradation mechanisms of halophilic microorganisms is also limited. In this review, we discuss recent research on the removal of organic pollutants such as organic matter, in terms of chemical oxygen demand (COD), dyes, hydrocarbons, N-aliphatic and N-aromatic compounds, and phenols, in conditions of high salinity. In addition, some proposal pathways for the degradation of aromatic compounds are presented.

Recent studies in microbial degradation of petroleum hydrocarbons in hypersaline environments

Many hypersaline environments are often contaminated with petroleum compounds. Among these, oil and natural gas production sites all over the world and hundreds of kilometers of coastlines in the more arid regions of Gulf countries are of major concern due to the extent and magnitude of contamination. Because conventional microbiological processes do not function well at elevated salinities, bioremediation of hypersaline environments can only be accomplished using high salt-tolerant microorganisms capable of degrading petroleum compounds. In the last two decades, there have been many reports on the biodegradation of hydrocarbons in moderate to high salinity environments. Numerous microorganisms belonging to the domain Bacteria and Archaea have been isolated and their phylogeny and metabolic capacity to degrade a variety of aliphatic and aromatic hydrocarbons in varying salinities have been demonstrated. This article focuses on our growing understanding of bacteria and archaea responsible for the degradation of hydrocarbons under aerobic conditions in moderate to high salinity conditions. Even though organisms belonging to various genera have been shown to degrade hydrocarbons, members of the genera Halomonas Alcanivorax, Marinobacter, Haloferax, Haloarcula, and Halobacterium dominate the published literature. Despite rapid advances in understanding microbial taxa that degrade hydrocarbons under aerobic conditions, not much is known about organisms that carry out similar processes in anaerobic conditions. Also, information on molecular mechanisms and pathways of hydrocarbon degradation in high salinity is scarce and only recently there have been a few reports describing genes, enzymes and breakdown steps for some hydrocarbons. These limited studies have clearly revealed that degradation of oxygenated and non-oxygenated hydrocarbons by halophilic and halotolerant microorganisms occur by pathways similar to those found in non-halophiles.

Bacterial Biodegradation of Crude Oil Using Local Isolates

An experimental study was undertaken to assess the efficiency of Pseudomonas aeruginosa, Bacillus subtilis, and Acinetobacter lwoffi isolated from petroleum contaminated water and soil samples to degrade crude oil, separately and in a mixed bacterial consortium. Capillary gas chromatography was used for testing the effect of those bacterial species on the biodegradation of crude oil. Individual bacterial cultures showed less growth and degradation than did the mixed bacterial consortium. At temperature 22°C, the mixed bacterial consortium degraded a maximum of 88.5% of Egyptian crude oil after 28 days of incubation. This was followed by 77.8% by Pseudomonas aeruginosa, 76.7% by Bacillus subtilis, and 74.3% by Acinetobacter lwoffi. The results demonstrated that the selected bacterial isolates could be effective in biodegradation of oil spills individually and showed better biodegradation abilities when they are used together in mixed consortium.

Biofilm-mediated enhanced crude oil degradation by newly isolated pseudomonas species

The bioavailability of organic contaminants to the degrading bacteria is a major limitation to efficient bioremediation of sites contaminated with hydrophobic pollutants. Such limitation of bioavailability can be overcome by steady-state biofilm-based reactor. The aim of this study was to examine the effect of such multicellular aggregation by naturally existing oil-degrading bacteria on crude oil degradation. Microorganisms, capable of utilizing crude oil as sole carbon source, were isolated from river, estuary and sea-water samples. Biochemical and 16S rDNA analysis of the best degraders of the three sources was found to belong to the Pseudomonas species. Interestingly, one of the isolates was found to be close to Pseudomonas otitidis family which is not reported yet as a degrader of crude oil. Biodegradation of crude oil was estimated by gas chromatography, and biofilm formation near oil-water interface was quantified by confocal laser scanning microscopy. Biofilm supported batches of the isolated Pseudomonas species were able to degrade crude oil much readily and extensively than the planktonic counterparts. Volumetric and topographic analysis revealed that biofilms formed in presence of crude oil accumulate higher biomass with greater thickness compared to the biofilms produced in presence of glucose as sole carbon source.

Biodegradation of benzene homologues in contaminated sediment of the East China Sea

This study focused on acclimating a microbial enrichment to biodegrade benzene, toluene, ethylbenzene and xylenes (BTEX) in a wide range of salinity. The enrichment degraded 120 mg/L toluene within 5d in the presence of 2M NaCl or 150 mg/L toluene within 7d in the presence of 1-1.5M NaCl. PCR-DGGE (polymerase chain reaction-denatured gradient gel electrophoresis) profiles demonstrated the dominant species in the enrichments distributed between five main phyla: Gammaproteobacteria, Sphingobacteriia, Prolixibacter, Flavobacteriia and Firmicutes. The Marinobacter, Prolixibacter, Balneola, Zunongwangia, Halobacillus were the dominant genus. PCR detection of genotypes involved in bacterial BETX degradation revealed that the degradation pathways contained all the known initial oxidative attack of BTEX by monooxygenase and dioxygenase. And the subsequent ring fission was catalysed by catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. Nuclear magnetic resonance (NMR) spectroscopy profiles showed that the bacterial consortium adjusted the osmotic pressure by ectoine and hydroxyectoine as compatible solutes to acclimate the different salinity conditions.

Biodegradation of petroleum hydrocarbons in hypersaline environments

Literature on hydrocarbon degradation in extreme hypersaline media presents studies that point to a negative effect of salinity increase on hydrocarbonoclastic activity, while several others report an opposite tendency. Based on information available in the literature, we present a discussion on the reasons that justify these contrary results. Despite the fact that microbial ability to metabolize hydrocarbons is found in extreme hypersaline media, indeed some factors are critical for the occurrence of hydrocarbon degradation in such environments. How these factors affect hydrocarbon degradation and their implications for the assessment of hydrocarbon biodegradation in hypersaline environments are presented in this review.